Molecular dynamics simulations capture the behavior of biological macromolecules in full
atomic detail, but their computational demands, combined with the challenge of …

Simulating protein folding has been a challenging problem for decades due to the long
timescales involved (compared with what is possible to simulate) and the challenges of …

Markov State Models (MSMs) provide an automated framework to investigate the dynamical
properties of high-dimensional molecular simulations. These models can provide a human …

Molecular dynamics simulations hold the promise of providing an atomic-level description of
protein folding that cannot easily be obtained from experiments. Here, we examine the …

Characterizing the equilibrium ensemble of folding pathways, including their relative
probability, is one of the major challenges in protein folding theory today. Although this …

The high arithmetic performance and intrinsic parallelism of recent graphical processing
units (GPUs) can offer a technological edge for molecular dynamics simulations. ACEMD is …

Molecular dynamics simulations allow for atomic-level characterization of biomolecular
processes such as the conformational transitions associated with protein function. The …

Quantitatively accurate all-atom molecular dynamics (MD) simulations of protein folding
have long been considered a holy grail of computational biology. Due to the large system …

Anton is a recently completed special-purpose supercomputer designed for molecular
dynamics (MD) simulations of biomolecular systems. The machine's specialized hardware …

A central quantity of interest in molecular biology and medicine is the free energy of binding
of a molecule to a target biomacromolecule. Until recently, the accurate prediction of binding …